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REVIEWS

Non-small-cell lung cancers:


a heterogeneous set of diseases
Zhao Chen1*, Christine M. Fillmore2,3,4*, Peter S. Hammerman1, Carla F. Kim2,3,4 and
Kwok-Kin Wong1,5,6
Abstract | Non-small-cell lung cancers (NSCLCs), the most common lung cancers, are known
to have diverse pathological features. During the past decade, in-depth analyses of lung
cancer genomes and signalling pathways have further defined NSCLCs as a group of distinct
diseases with genetic and cellular heterogeneity. Consequently, an impressive list of
potential therapeutic targets was unveiled, drastically altering the clinical evaluation and
treatment of patients. Many targeted therapies have been developed with compelling
clinical proofs of concept; however, treatment responses are typically short-lived. Further
studies of the tumour microenvironment have uncovered new possible avenues to control
this deadly disease, including immunotherapy.

Lung cancer results in the largest number of cancer- and tumour microenvironment studies might be used
related deaths worldwide1,2. More than 85% of those to improve the survival of patients with NSCLC through
cases are currently classified as non-small-cell lung the development of novel therapeutic strategies.
cancer (NSCLC), for which the predicted 5‑year sur-
vival rate is 15.9% — a figure that has only marginally Defining NSCLC subsets
improved during the past few decades3. Technological NSCLC is currently defined by pathological character­
1
Department of Medical
Oncology, Dana-Farber advances during the past decade, including the intro- istics. The two predominant NSCLC histological pheno-
Cancer Institute, Boston, duction of next-generation sequencing (NGS), the types are adenocarcinoma (ADC; ~50%) and squamous
Massachusetts 02115, USA. generation of multiple genetically engineered mouse cell carcinoma (SCC; ~40%)4,5. In general, ADCs arise in
2
Stem Cell Program, Boston models (GEMMs) of lung cancer and the construction more distal airways, whereas SCCs arise in more proxi-
Children’s Hospital, Boston,
Massachusetts 02115, USA.
of large databases characterizing the molecular fea- mal airways and are more strongly associated with smok-
3
Harvard Stem Cell Institute, tures of human tumours, have transformed our view of ing and chronic inflammation than ADCs4,5. ADCs often
Cambridge, Massachusetts NSCLC from histopathological descriptions to precise have glandular histology and express biomarkers that
02138, USA. molecular and genetic identities that can be resolved to are consistent with an origin in the distal lung, includ-
4
Department of Genetics,
the single-cell level. In parallel, approaches and concepts ing thyroid transcription factor 1 (TTF1; also known
Harvard Medical School,
Boston, Massachusetts from fields such as developmental biology, stem cell biol- as NKX2‑1) and keratin 7 (KRT7)4,5. By contrast, SCCs
02115, USA. ogy and immunology have deepened our knowledge of are characterized by squamous differentiation, which is
5
Department of Medicine, tumour development, cellular heterogeneity and inter- more reminiscent of the pseudostratified columnar epi-
Harvard Medical School, actions between the lung tumour and its surrounding thelium that lines the trachea and upper airways4,6. SCCs
Boston, Massachusetts
02115, USA.
microenvironment. These multidisciplinary efforts are distinguished from ADCs in the clinic by immuno­
6
Belfer Institute for Applied have enhanced our understanding of molecular disease staining for cytokeratin 5 and cyto­keratin 6 and/or
Cancer Science, Dana-Farber mechanisms, thereby forming the rationales for target- the transcription factors SRY-box 2 (SOX2) and p63
Cancer Institute, Boston, ing different cellular compartments simultaneously. (REFS 4,5,7). Other subtypes of NSCLC include large cell
Massachusetts 02115, USA.
Scientists and physicians have better tools than ever to carcinoma, which is diagnosed by exclusion if tumour
*These authors contributed
equally to this work. pursue answers to two provocative questions: first, how cells do not appear glandular or squamous in shape or
Correspondence to P.S.H., can we define the specific subsets of NSCLC that differ express ADC or SCC biomarkers, although it is unclear
C.F.K. and K.-K.W. by cellular and molecular composition? Second, how whether large cell carcinomas are genetically distinct
e‑mails: phammerman@ can we effectively control lung cancer growth for each from ADC or SCC4. Some neuroendocrine tumours
partners.org; carla.kim@
childrens.harvard.edu;
specific subset of NSCLC? In this Review, we discuss are also classified as NSCLC, although the most aggres-
kwong1@partners.org how data that are derived from technological advances sive form of neuroendocrine tumour is classified as
doi:10.1038/nrc3775 in lung cancer genomics, mouse modelling of cancers small-cell lung cancer (SCLC)4.

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Genetic mutations and genomic heterogeneity. the net effects of genotype and therapy response may be
Although histological features and marker expression achieved and will ultimately inform the most suitable
remain the basis of clinical tumour diagnosis, recent treatment strategies.
advances in NGS and other high-throughput genomic Other novel technologies have also facilitated the
profiling platforms have allowed researchers to exam- discovery and validation of somatic mutations in lung
ine the breadth of genetic mutations within lung cancer. For example, high-throughput screens using
tumours. Following the identification of KRAS and established short hairpin RNA (shRNA) libraries have
BRAF mutations8,9, epidermal growth factor receptor identified genes that cause synthetic lethality with
(EGFR) mutations were discovered in patients with common oncogenic events, such as KRAS-activating
lung ADC and were associated with response to EGFR mutations or p53 inactivation, leading to potential
inhibitors10–13. Further recurrent mutations and ampli- new treatment targets, such as TANK-binding kinase 1
fications in many potentially targetable oncogenes have (TBK1)32. Similarly, the application of mass spectro­
since been identified in lung ADC, including HER2 metry to metabolomic, proteomic and phosphoki-
(also known as ERBB2), MET, fibroblast growth fac- nase profiling, as well as single cell time-of-flight mass
tor receptor 1 (FGFR1) and FGFR2, as well as fusion cytometry (cyTOF), have led to numerous new findings,
oncogenes involving anaplastic lymphoma kinase including the discovery of recurrent aberrations such as
(ALK), the ROS1 receptor tyrosine kinase, neuregu- the ROS1 fusions and the potential diagnostic or prog-
lin 1 (NRG1), neurotrophic tyrosine kinase recep- nostic marker isocitrate dehydrogenase 1 (IDH1)17,33,34.
tor type 1 (NTRK1) and RET 14–22. These oncogenic Such advances in high-throughput technology are pro-
changes, many of which predict sensitivity to clini- moting rapid advances in our understanding of NSCLC
cal inhibitors, jointly account for most cases of lung biology and, ultimately, will help to determine how
ADC23–25. For lung SCC, the number of tumours for NSCLC develops, spreads and can be better treated.
which whole-exome sequencing is available is lower
than for ADC but, so far, potentially targetable muta- Heterogeneity in lung tumour microenvironments.
tions in ADC do not seem to be prevalent in this The concept of tumour heterogeneity applies not only
histological subtype20. Instead, genes such as discoi- to tumour epithelial cells but also to the diverse micro-
din domain-containing receptor 2 (DDR2), FGFR1, environments with which the tumour cells interact 35.
FGFR2, FGFR3 and genes in the PI3K pathway seem Carcinoma cells, in the lung and other organs, are closely
to be more commonly mutated in lung SCC20. Many associated with the extracellular matrix (ECM), mesen-
of these mutations (with the exception of those in chymal cells such as fibroblasts, infiltrating immune cells
the PI3K pathway) have been validated by preclinical and vasculature (FIG. 1). In some cases, this environment
studies as driver mutations22,26,27. is essential to tumour initiation or tumour growth,
NGS studies have also revealed the molecular tax- whereas in other cases it can prevent tumorigenesis or
onomy of lung cancer and have shown a dazzling com- even promote tumour clearance35,36.
plexity of somatic alterations in NSCLCs that extends In lung tumorigenesis, genesis of new blood and lym-
far beyond protein kinases to include epigenome phatic vessels supplies necessary nutrients for tumour
modifiers, transcription factors, splicing factors and growth and allows for an influx of immune cells of the
genes involved in cellular immunity 20,28,29. Potentially myeloid and lymphoid lineages. The myeloid cells that
important mutations and copy number gains identified are implicated in this process include tumour-associated
from patient tumours are summarized in TABLE 1, with macrophages (TAMs) and tumour-associated neutro-
relevant preclinical and clinical evidence. Among the phils37. Mice that harboured germline knock‑in of kinase-
21 different tumour types for which exome sequences dead inhibitor of nuclear factor-κB (NF‑κB) kinase
were directly compared, lung SCC and ADC ranked subunit-α (IKKα) developed spontaneous lung SCC
second and third highest in median somatic muta- that is characterized by NF‑κB activation and marked
tion frequency, with an average of ten mutations per accumulation of TAMs that were essential for disease
megabase of coding DNA sequenced30. It is worth progression38. Secretion of pro-angiogenic factors such
noting that ADCs in non-smokers have 5–6‑times as platelet-derived growth factor (PDGF) and vascular
fewer mutations24,31. Given this relatively large num- endothelial growth factor (VEGF) by TAMs in lung can-
ber of mutations per tumour, there will probably be cer suggests why these cells are associated with increased
more important mutations identified for NSCLC as microvessel formation39,40. Likewise, increased neutro-
the number of tumours that are analysed increases. phil numbers have been associated with poor prognosis
An important challenge that remains is understanding in NSCLCs, perhaps owing to their ability to degrade
which of these many mutations are important in lung matrices with elastase41,42. Neutrophils that are found
Myeloid-derived
carcinogenesis and/or treatment response, in contrast in mouse tumours are phenotypically characterized as
suppressor cells
(MDSCs). MDSCs encompass a to those mutations that are merely a consequence of polymorphonuclear CD11B- and lymphocyte antigen
heterogeneous population of the tumorigenic process. Thus, the genomic profiles 6G‑expressing (CD11B+Ly6G+) cells, and are often con-
myeloid cells, which share the highlight the heterogeneity of the NSCLC genome and sidered to be a subtype of myeloid-derived suppressor cells
ability to suppress T cells provide a plausible explanation for the highly hetero- (MDSCs)43. In the tumour microenvironment, accu-
through the production of
arginase and the expression
geneous treatment responses that we have observed in mulated MDSCs are thought to promote tumour pro-
of inducible nitric oxide the clinic. By cataloguing a large collection of muta- gression by increasing matrix degradation, tumour cell
synthase (iNOS). tions for each patient, a more accurate evaluation of proliferation, metastasis and angiogenesis35,37.

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Table 1 | Potential important alterations in ADC and SCC


Gene Status Frequency (%) Available GEMMs Currently Selected potential Refs
(M, C available targeted targeted therapies
or F)* ADC SCC therapies Preclinical Clinical
evidence evidence
Receptor tyrosine kinases
EGFR M or C 10 (M) 2–3 L858R, Del19, T790M and Erlotinib, gefitinib AZD9291, CO‑1686 and 126 11
Ins20 and afatinib HM61713
FGFR1 C N/A 20 N/A N/A Dovitinib, ponatinib, AZD4547 150 22
and BGJ398
FGFR2 M or C 3 (M) 3 N/A N/A Dovitinib, ponatinib, AZD4547 151 20
and BGJ398
ALK F 3–5 <1 ALK fusion, L1196M and Crizotinib and AP26113, alectinib, 125 18
F1174L ceritinib ganetespib and PF‑06463922
MET C 2–4 N/A Overexpression Crizotinib Tivantinib, cabozantinib, 152 14
INC280 and onartuzumab
ROS1 F 1–2 N/A N/A Crizotinib PF‑06463922 153 17
NTRK1 F 1–2 N/A N/A N/A Crizotinib and lestaurtinib 21 21
RET F 1 N/A N/A N/A Carbozantinib and vandetanib 154 16
HER2 M or C 2–4 N/A HER2-YVMA insertion N/A Neratinib, afatinib, lapatinib 155 19
(M) and trastuzumab
DDR2 M N/A 2–3 N/A N/A Dasatinib 27 27
PDGFRA M 6–7 4 N/A N/A Sunitinib 156 28
Signalling
KRAS M 15–25 1–2 G12D, G12C and G12V N/A Selumetinib plus docetaxel 157 158
combination
NF1 M 12 10 Null N/A 159 28
BRAF M 1–6 4–5 V600E N/A Vemurafenib, dabrafenib and N/A 160
trametinib
PIK3CA M 5 15 p110α N/A BEZ235, BKM120 and 99 161
GDC0941
MEK1 M 1 N/A N/A N/A Selumetinib and trametinib N/A 162
NOTCH1 M 8 1 Conditional null N/A N/A 163 164
Epigenetic factors
MLL2 M 9 20 N/A N/A N/A 165 28
EZH2 M 2 2 N/A N/A N/A 166 28
TET2 M 3 2 N/A N/A N/A 167 28
DNMT3A M 4 1 N/A N/A N/A 168 28
Transcription factors
SOX2 C 6 65 Overexpression N/A N/A 7 103
MYC C 25 N/A Overexpression N/A N/A 133 104
Proteolysis
KEAP1 M 17 12 N/A N/A N/A 169 170
Cell cycle
CDKN2A M 7 15 Null N/A N/A 171 172
Ligand
NRG1 F <1 N/A N/A N/A N/A 15 15
Tumour suppressor
TP53 M 52 79 Conditional null and R172H N/A N/A 98 173
LKB1 M 9 2 Conditional null N/A N/A 65 174
PTEN M 2 8 Conditional null N/A BEZ235, BKM120 and 175 176
GDC0941
ADC, adenocarcinoma; ALK, anaplastic lymphoma kinase; CDKN2A, cyclin-dependent kinase inhibitor 2A (which encodes INK4A and ARF); DDR2, discoidin
domain-containing receptor 2; Del19, EGFR exon 19 deletion; DNMT3A, DNA (cytosine‑5-)-methyltransferase 3α; EGFR, epidermal growth factor receptor;
EZH2, enhancer of zeste homologue 2; FGFR1, fibroblast growth factor receptor 1; GEMM, genetically engineered mouse model; Ins20, EGFR exon 20 insertion;
KEAP1, kelch-like ECH-associated protein 1; LKB1, liver kinase B1; MLL2, mixed-lineage leukaemia 2; N/A, not available; NF1, neurofibromin 1; NRG1, neuregulin 1;
NTRK1, neurotrophic tyrosine kinase, receptor, type 1; PDGFRA, platelet-derived growth factor receptor-α; PIK3CA, PI3K catalytic subunit-α; SCC, squamous cell
carcinoma; SOX2, SRY-box 2; TET2, TET methylcytosine dioxygenase 2. *Status refers to mechanisms by which each gene is altered in tumours — mutation (M),
copy number gain (C) or fusion (F).

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Endothelial PDGF Macrophage Differences in the ability to secrete inflammatory


cell cytokines such as interleukin‑6 (IL‑6) may be one way
VEGF ECM: keratin,
Fibroblast fibronectin in which tumour cells influence their surroundings50,51.
and collagen Tumours that are driven by different oncogenic muta-
Erythrocyte tions in mice, such as EGFR and Kras, have distinguish-
Tumour cell
able immune infiltrates with respect to cell types and
their phenotypes in the tumour immune microenviron-
PDL1 ment 48,49. These mechanisms have not been defined in
detail, and there are other important questions to con-
Neutrophil PD1 sider: does each genetic subset of NSCLC have its own
CD8+
unique microenvironmental influences, or can common
T cell characteristics of how the surroundings drive tumour
CXCR2 CXCL
subsets be uncovered? How does targeted therapy alter
Figure 1 | The lung cancer microenvironment.  The tumour microenvironment,
Nature Reviews | Cancer the tumour microenvironment? Do drug-resistant or
including endothelial cells, fibroblasts and myeloid cells, among others, has important recurrent tumours have an environmental milieu that is
roles in determining the characteristics of lung tumours. It is likely that a combination distinct from the initial untreated tumour? A more thor-
of the cell of origin, genetic alterations and microenvironmental factors all contribute to ough understanding of these dynamic interactions will
the lineage identity of lung tumours. Extracellular matrix (ECM), which often consists of help to show new targets that can be manipulated to pro-
keratins in lung squamous cell carcinoma and fibronectin in desmoplastic lung
mote antitumor effects. Importantly, many of these ques-
adenocarcinomas, gives structural support to tumour cells and is associated with
tumour-associated fibroblasts. Blood vessels are newly formed at the tumour site by
tions are challenging to understand, given the need to
recruitment of endothelial cells via platelet-derived growth factor (PDGF) and vascular study the immune system in vivo, and the use of mouse
endothelial growth factor (VEGF), among others. As the blood and lymphatic vessels models with intact immune systems in combination with
form, numerous blood cells, including macrophages, neutrophils, T cells and B cells, patient samples may be instructive.
home to the tumours. In particular, tumours can recruit neutrophils through secretion of
CXC-chemokine ligand (CXCL) family members, which bind to the neutrophil receptor Cell(s) of origin for NSCLC heterogeneity at tumour ini-
CXCR2. In addition, tumour cells often express immune checkpoint molecules, such as tiation. Another contributing factor to the diversity of
programmed cell death 1 ligand 1 (PDL1), to attenuate a cytotoxic response from T cells. NSCLCs may be the potential distinct cells of origin in
PD1, programmed cell death 1. which subsets of NSCLC first arise. The cell of origin for
each subset of NSCLC is essentially unknown beyond
Tumours can evade immune surveillance by initial work in this area in mouse models. For example,
expressing molecules that maintain tolerance to nor- it remains to be understood whether multiple cell types
mal peripheral tissues, including the interaction of the are equally likely to produce KRAS-mutant ADC or if
tumour-associated programmed cell death 1 ligand 1 only one cell type exists in the right microenvironment
(PDL1) with the immune receptor programmed cell and must gain oncogenic KRAS expression to produce
death 1 (PD1; also known as PDCD1). Recently, the this type of ADC. It is possible that the biology of differ-
use of antibodies targeting the PD1–PDL1 checkpoint ent cells of origin is what drives the different phenotypes
has resulted in some marked responses in early-stage of NSCLCs with distinct genotypes. This could be the
clinical trials for a large panel of therapy-refractory can- result of unique gene expression patterns of the originat-
cer subtypes, including advanced melanoma, NSCLC ing cells, differences in the type of cells that the originating
and renal cell cancer, with a proportion of responding cells can produce, or unique microenvironments of the
patients showing persistent long-term benefits44,45. The originating cell type. Ultimately, the clinical importance
PD1–PDL1 interaction inhibits CD8+ cytotoxic T lym- behind these seemingly basic biological questions is
phocyte proliferation, survival and effector function, whether a different cell of origin partly dictates treat-
and can induce apoptosis of tumour-infiltrating T cells; ment responses. Can knowledge of the cell of origin pre-
PD1–PDL1 interactions can also promote the differen- dict environmental influences that can be targeted for
tiation of CD4+ T cells into forkhead box P3‑expressing antitumour therapy? Furthermore, can knowledge of the
(FOXP3+) regulatory T (TReg) cells, which are known to cell of origin be used for the earlier detection of tumours?
further suppress the immune system and cause periph- The answers to these questions have the capacity to
eral immune tolerance in patients with lung cancer 46. revolutionize our current concept of the stratification,
Despite the promising clinical benefits, there is currently diagnosis and treatment of NSCLC.
no defined subset of patients with lung cancer who are A long-standing hypothesis proposes that stem and
particularly sensitive to PD1–PDL1 blockade. This is progenitor cells in adult tissues function as carcinoma
partly due to a lack in the understanding of how tumour cells of origin because they are the only cells that have a
cells affect their microenvironment, including the sur- sufficient lifespan to accumulate the many genetic altera-
rounding immune cells44,45,47. Evaluating the expres- tions required for tumour progression52. Furthermore,
sion of PDL1 on tumour cells is only the starting point stem cells have inherent self-renewal capacity and may
in the analysis of the interactions between tumour cells not need extensive epigenetic reprogramming. However,
and the surrounding microenvironment 48,49. Many even genetically normal cells with limited self-renewal
important questions remain, including whether lung capacity can be induced to acquire more stem cell-like
tumours with distinct genetic backgrounds differ in how properties in response to genetic alterations or micro­
they shape their immune microenvironment. environmental changes53,54, and this supports the idea that

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Box 1 | Mouse models


such as AT2 cells and BASCs, AT2 cells seemed to be the
only cells that were capable of giving rise to advanced
Genetically engineered mouse models (GEMMs) have enabled numerous studies of ADC in the alveolar space, whereas club cells and BASCs
non-small-cell lung cancer (NSCLC) that would not be possible using patient samples or seemed to be limited to driving bronchiolar hyperplasia
cancer cell lines: for example, preclinical or co‑clinical trials of targeted therapies, the
within the same time frame59. Using these approaches, it
study of metastatic and transplanted disease and examination of tumour cells of
origin25,49,74,98,125,126. Today, GEMMs for most of the common NSCLC driver mutations
is notable that changes in the cells of origin were evident
have been generated, including for KRAS, epidermal growth factor receptor (EGFR), when the genotype for tumour initiation was altered (for
and echinoderm microtubule-associated protein-like 4 (EML4)–anaplastic lymphoma example, to include p53 loss) or if injury or inflamma-
kinase (ALK); and despite their lack of genetic complexity compared to human cancers, tion were present during tumour initiation (for example,
they have shown some remarkable similarities in pathological features and treatment after adenovirus infection or after naphthalene-induced
responses to the human disease98,125–127. injury)56,59–63. Injury or inflammation probably more
GEMMs are particularly informative when the net effects of several mutations need to closely mimics the scenario of tumour initiation in
be determined in vivo. For example, the conditional oncogenic KrasG12D mouse model humans, in which environmental influences and ongo-
has been used to elucidate the steps from early to late tumorigenesis, owing to the ing injury occur in contrast to the relatively sterile mouse
temporal control it affords128, and it is easy to combine with mice bearing conditional
colony. These questions are unexplored in other models
null alleles for other genes of interest. For example, KrasG12D tumours only reach a full
adenocarcinoma stage with a very long latency, but KrasG12D-expressing and Trp53‑null
of ADC that use distinct oncogenes or in SCC. Thus, it
tumours are more advanced and show a decreased response to certain treatment remains entirely possible that club cells, AT2 cells and
strategies when compared to KrasG12D tumours128,129. Simultaneous inactivation of BASCs are all possible initiators of lung ADC. Future
Pten and liver kinase B1 (Lkb1) in the lung produced only squamous cell carcinoma development of more precise lineage-specific Cre driv-
(SCC)49, and this fits with the preclinical observations that PI3K and mTOR pathways are ers combined with approaches to study tumorigenesis
activated in most human lung SCC tumours20,49,65. Similar genetic breeding schemes can in the context of injury and inflammation (situations
be used to identify and validate potential treatment targets through in vivo synthetic that are more likely to mimic carcinogenesis in humans)
lethal experiments. Elegant studies have recently shown that MYC, cyclin-dependent will be needed to better determine the comparable
kinase 4 (CDK4) and CRAF are crucial KRAS effectors that can lead to synthetic lethality ADC-initiating activity of these populations.
when genetically inactivated in tumours with activated KRAS130–134.
Although increasing amounts of genomic data show
The assessment of immunotherapeutics and the dynamic interactions between
tumour cells and their microenvironment using GEMMs (which are immunocompetent)
that distinct gene expression programmes and driver
is another emerging research direction. Experiments of particular interest include gene mutations distinguish ADC from SCC, it remains unclear
expression and pathway activation profiles for each cell type within the tumour; whether these two tumour types arise from a common
genotype- or treatment-dependent influences on the tumour microenvironment; and cell of origin or diverse cell types, including different lung
effects of individual or combination therapies on tumour cells, immune cells and other stem or progenitor cells (BOX 2). Until recently, a paucity of
cell types within the tumour microenvironment. GEMMs for SCC has precluded analysis of the cells
Patient-derived xenograft (PDX) models provide an alternative and complementary of origin of this important NSCLC subtype. It has long
method to GEMMs to address human–murine differences and allow for expansion of been hypothesized that SCC arises from basal cells, as
patient material to perform assays such as metabolomic and serial transplantation135. lung SCCs most frequently arise in the proximal lung 4,
A ‘humanized’ lung and even a ‘humanized’ immune system in the mouse might offer a
but also because they often express KRT5, SOX2 and
more accurate means to model NSCLC.
p63, which are markers of the normal basal cell popula-
tion5–7,62,64. GEMMs of ADC have been more widespread,
more mature, differentiated cells may be just as likely to mostly owing to the usefulness and availability of the con-
give rise to malignancy. Historically, ADCs have been pro- ditional oncogenic Kras allele (which drives lung ADCs
posed to arise from club cells (previously known as Clara both independently and more rapidly in combination
cells) or alveolar epithelial type 2 (AT2) cells, owing to with Trp53 loss) as well as early models using chemicals
the staining of patient ADCs by immunohisto­chemistry that induce RAS mutations to drive tumours. Although
with markers of these cell types4,5. However, it is impor- KRAS or NRAS mutations are present in up to 25% of
tant to note that the staining pattern of a tumour is merely ADCs, they are rarely detected in SCCs, and mouse
a snapshot of the gene expression of the tumour cells modelling with these oncogenes seems to result predomi-
at that time point and might not match the initiating nantly in the development of ADC. Mutations that are
cell type. Our current understanding of cells of origin common in samples from patients with SCC have only
for lung cancer is mostly derived from experimental recently been catalogued, and this opens up new ideas
data using GEMMs55 (BOX 1; FIG. 2). Many conditional about how to model SCC20. Kinase-dead IKKα knock‑in
GEMMs target activation and/or loss of genes specifically mice develop spontaneous lung SCC, but because this
to lung cells by intranasal or intratracheal instillation of mouse has a germline Ikka mutation, it is not clear which
adenovirus-Cre, which infects lung epithelial cells along cells in the lung expanded into the squamous tumours38.
the proximal to distal tract. After using intra­nasal adeno­ Loss of the tumour suppressor liver kinase B1 (Lkb1; also
virus-Cre to induce oncogenic Kras, loss of Pten or loss known as Stk11) in the oncogenic KrasG12D model pro-
of p38, the first hyperproliferative cells to be observed duces a mixture of tumours, including ADC, SCC and
were bronchioalveolar stem cells (BASCs) — implicat- large cell carcinoma65. Similarly, a mixture of ADC
ing them as possible ADC cells of origin56–58. However, and SCC is found in mice after targeted deletion of Pten
in more recent studies that targeted the expression of or transforming growth factor-β receptor 2 (Tgfbr2)
oncogenic KrasG12D only in cells expressing club cell in proximal cells with keratin-driven Cre alleles in the
secretory protein (CCSP), such as club cells and BASCs, KrasG12D background66. Expression of the transcription
or only in cells expressing surfactant protein C (SPC), factor Sox2 (overexpressed in 20–60% of human SCCs) in

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Proximal Basement Pseudostratified


membrane columnar epithelium
Cartilage Club cell (CCSP+)
Ciliated cell (AcTUB+)
Goblet cell
Basal cell (KRT5+ and p63+)

Typical SCC Modelled by:


• SOX2+ • KrasG12D expression
• p63+ and Lkb1-null
• KRT5+ • Lkb1-null and Pten-null
• IKKα: kinase dead

Alveolar space AT2 (SPC+)


BASC
(CCSP+ and SPC+)
AT1
Distal

Simple columnar epithelium


Typical ADC Modelled by:
• KrasG12D
Neuroendocrine • TTF1+ • KrasG12D expression
cell (CGRP+) • KRT7+ and Trp53-null
• SPC+ • EGFRT790M/L858R
• Many others

Figure 2 | A diagram of proximal and distal lung cells, indicating markers that are retained in carcinomas and
putative squamous cell carcinoma (SCC) and adenocarcinoma (ADC) cells of origin.  DiverseNature Reviews | Cancer
lung stem or progenitor
cell populations are thought to have the ability to drive lung oncogenesis in different contexts. In the proximal lung, the
tracheal basal cell has been proposed to be the cell of origin for lung SCC. The evidence for this relationship includes
the expression of p63, SRY-box 2 (SOX2) and keratin 5 (KRT5) within the basal cells, squamous metaplasia of the basal cells
(common in smokers), and squamous cell carcinomas. Squamous tumours are modelled in mice by KrasG12D expression and
liver kinase B1 (Lkb1) knockout (20% of lesions are squamous), knocking in a germline dominant-negative kinase-dead
inhibitor of nuclear factor-κB kinase subunit-α (IKKα) and knocking out both Lkb1 and Pten (100% of lesions are squamous
for the second two models). Two bronchiolar cell populations, the bronchiolar progenitor cells and the bronchioalveolar
stem cells (BASCs) may also be able to give rise to tumours with squamous characteristics, although experimental lineage
tracing is needed to confirm this theory. ADCs can be modelled by KrasG12D expression (long latency), KrasG12D expression
and Trp53‑null, and epidermal growth factor receptor (EGFR)T790M/L858R, among other genetic models, and they are thought
to arise from more proximal airway cells. These tumours often retain characteristics of proximal airways, such as the
expression of surfactant protein C (SPC), KRT7 and thyroid transcription factor 1 (TTF1). Again, BASCs or bronchiolar
progenitor cells, which are able to give rise to alveolar lineages after lung injury, may likewise be able to give rise to
tumours with alveolar characteristics. AcTUB, acetylated tubulin; AT, alveolar epithelial type; CCSP, club cell secretory
protein; CGRP, calcitonin gene-related peptide.

club cells and BASCs produces lung tumours that express transplantation assays. Establishment of tumours at
the marker p63 but histologically resemble ADCs7. This metastatic sites and tumour recurrence following treat-
intriguing finding suggests that distal lung epithelia are ment have been attributed to growth and survival of
unable to produce a fully squamous phenotype, despite the TPCs67,68. Recent studies have identified potential cell
expression of an SCC transcription factor. In addition, surface markers or genetic traits that may mark the TPC
the deletion of Lkb1 and Pten in the lung via intranasal population in NSCLC, such as aldehyde dehydroge-
adenovirus-Cre was recently shown to give rise to fully nase (ALDH) activity or expression of NOTCH, CD24,
penetrant lung SCCs49. The next important step will be to CD166 or CD44 (REFS 38,69–73). However, these stud-
use lineage-restricted Cre alleles, such as the oestrogen- ies have not used serial transplant assays in the context
responsive Cre under control of the Krt5 promoter of the lung environment, and a bona fide human lung
(Krt5–Cre-ER), to determine which lung cells that are TPC remains to be defined. GEMMs have allowed for
null for Lkb1 and Pten are able to drive squamous disease. more systematic study of lung TPC phenotypes, includ-
ing serially transplanted tumours and metastases. Studies
Tumour-propagating cells (TPCs) and cellular plastic- in the KrasG12D-expressing and Trp53‑null model of ADC
ity: heterogeneity between tumour cells. ‘Cancer stem suggest that stem cell antigen 1 (SCA1, also known as
cells’ or TPCs, which are defined as the tumour cells Ly6A)+, CD24+, β4 integrin+, and NOTCH3hi mark
with the stem cell-properties of self-renewal and dif- the TPC population70,73. The identity of TPCs from
ferentiation, have the capacity to produce tumours in other ADC GEMMs is unknown; SCA1 did not enrich

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Box 2 | Lung stem and progenitor cell populations


after therapy 75. Further careful evaluation of TPC activ-
ity and cellular plasticity of tumour cells with patient
Genetic lineage tracing and cell biology approaches have shown that the murine lung tissues, probably using patient-derived xenograft (PDX)
contains region-specific stem and progenitor cell populations that respond to local
models and GEMMs of lung cancer, will help us to better
injury. Basal cells function as stem cells for the trachea, main bronchi and upper airways,
where they can replace the pseudostratified epithelium, including secretory club cells
understand tumour lineage conversion as a path towards
(previously known as Clara cells), mucus-producing goblet cells and ciliated cells136–138. developing chronic treatment resistance. These findings
In more distal airways, club cells are a self-renewing population that maintains the also highlight the importance of considering how cells of
ciliated cells139, and subsets of club cells, such as bronchiolar progenitors, can give rise origin may differ, depending on the therapeutic status
to ciliated and club cell lineages after injury140,141. In the alveolar space, where gas of the tumour environment.
exchange is carried out by alveolar epithelial type 1 (AT1) cells, the surfactant-
expressing AT2 cells can function as stem cells60,142. Another alveolar cell Integrated therapies for NSCLC
population, expressing α6β4 integrin, can also produce alveolar epithelia142,143. Target validation and patient stratification. Although
Bronchioalveolar stem cells (BASCs), which reside between the airway and alveolar studies of lung cancer genomes have implicated several
space, can give rise to both epithelial lineages56,114,144–146. Murine proximal and distal
genes as likely crucial mediators of tumour initiation and
lung stem cells can be isolated by fluorescence-activated cell sorting that uses different
cell surface markers and can be grown in three-dimensional culture systems to study
progression, experimental validation of the most impor-
their differentiation potential114,136,141,147. Basal cells can be isolated from mouse or tant, functional genomic changes in lung cancer cells
human lung on the basis of their expression of nerve growth factor receptor remains a challenge. Despite computational approaches
(NGFR)136,148, and AT2 cells can be purified from distal lung — most recently with the to separate ‘driver’ alterations from passenger altera-
marker HTII‑280 (REF. 142). Several other human lung stem cell populations have been tions, this distinction is probably more nuanced, and
reported in the human lung, but their roles have been controversial149, and this points to substantial work will need to be completed to model the
the characterization of human lung stem and progenitor cells as an important area for consequences of specific genome alterations in NSCLC.
future research. Furthermore, precisely how these cell types change their lineage Existing repositories of lung cancer cell lines, as well as
potential in the face of oncogenic insult coupled with injury is unknown and is likely to efforts to generate new cell lines from patient tumours
influence tumorigenesis; injury and transformation might substantially alter plasticity53.
have led to a number of important discoveries, although
A better understanding of lung stem and progenitor cells and methods for their analysis
would open up new ways to explore the cellular origins of lung tumorigenesis.
these cell lines still fail to represent the full diversity of
human NSCLCs79. Three-dimensional culture techniques
might also offer a new way to propagate normal and
for TPCs from the Kras- or EGFR-driven GEMMs74. tumorigenic lung cells to better probe vulnerabilities of
In the first lung-specific genetic model of SCC (the Lkb1- tumour cells49,73. Multiple in vivo models using mice to
and Pten-null model) the TPCs had a high expression recapitulate lung cancer disease processes and treatment
of SCA1 and the basal cell marker nerve growth factor responses have been generated, including GEMMs har-
receptor (NGFR). Intriguingly, these TPCs also expressed bouring specific genetic aberrations that have been iden-
high levels of the immune-checkpoint molecule PDL1, tified in human tumours55,80 (BOX 1). Translation of the
which may be targetable as described above49. Overall, experimental results obtained through in vitro and in vivo
these findings indicate the importance of taking the modelling systems has formed the basis for current and
geno­type of the tumour into account when seeking to future patient stratification paradigms (BOX 3). The limi-
define a TPC population; each subset of NSCLC might tations of these approaches should also be considered in
harbour TPCs with unique surface markers and molec- future work to develop a more precise understanding of
ular drivers, which could each be uniquely targeted. how to predict therapy response.
Alternatively, many subsets of NSCLC might not have
one TPC population that can be defined. Future research Current treatments for NSCLC. The past decade has
focusing on resolving the metastatic activity and therapy seen some truly impressive new treatments for subsets of
response of murine TPCs and the molecules that control patients with lung cancer, most of whom harbour muta-
them may help to translate these findings to improve the tions in one of the key oncogenic driver mutants upon
treatment of patients with lung cancer. which tumour survival and progression are depend-
The genetic complexity and rapid clonal evolution ent. These include mutations in EGFR, the echinoderm
of lung tumours could mean that if TPCs do occur in microtubule-associated protein-like 4 (EML4)–ALK fusion
most lung cancers, they will have a high degree of plas- and ROS1 fusions81,82. Extensive preclinical and clinical
ticity. Fascinating clinical observations have shown some studies have proven the marked treatment responses and
patients who are initially diagnosed with EGFR-driven survival advantages over conventional chemotherapies
Pseudostratified epithelium ADCs develop SCLC after long-term treatment with the that are provided by target-specific inhibitors to EGFR-
This describes the epithelium EGFR tyrosine kinase inhibitors gefitinib or erlotinib75,76. activating mutations or to ALK fusions 83–85. Recent
of the trachea, which is truly a In contrast to ADC models, lineage tracing and viruses genomic analyses of lung SCC have also given the first
monolayer but appears to have
that are engineered to express Cre under the control of set of potentially targetable driver mutations, including
some stratification due to the
variable distances of the nuclei various cell-type-specific promoters have been used to FGFR1, FGFR2, FGFR3, DDR2 and PI3K20. Clinical trials
from the basal lamina. show that SCLCs probably arise from neuroendocrine that aim to target these subsets of patients who have Stage
cells76–78. However, examination of these tumours before I–IIIA lung cancers are currently underway; preliminary
Patient-derived xenograft and after SCLC conversion shows the persistence of the results were presented at the 2014 American Association
(PDX). Primary tumour cells
from fresh patient tumours that
same EGFR mutations, suggesting a shared clonal ori- for Cancer Research Annual Meeting86, and these showed
are propagated subcutaneously gin of both types of tumours. This highlights the poten- responses to an FGFR inhibitor (BGJ398) in a subset of
in immunocompromised mice. tial epigenetic plasticity of lung cells and lung tumours patients with SCC who have FGFR1 amplification.

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Box 3 | Patient stratification


resistance mechanism that is evident by an improved
response and survival in patients with EGFR mutations
Stratification and treatment selection for patients with non-small-cell lung cancer who have an increased expression of the NF‑κB inhibi-
(NSCLC) heavily relies on radiographical and pathological evaluation in standard tor IκBα (also known as NFKBIA)96. In addition, a com-
clinical practice. In recent years, molecular diagnostic platforms have been gradually mon BIM (also known as BCL2L11) polymorphism that
introduced into this process. Today, many cancer centres and hospitals have adopted
results in changes in splicing and the deletion of the pro-
some degree of genetic diagnosis. Commonly accepted oncogenic driver mutations,
including KRAS, epidermal growth factor receptor (EGFR), anaplastic lymphoma kinase
apoptotic BCL‑2‑homology domain (BH3) was shown to
(ALK), ROS and BRAF, are being sequenced and detected as a standard diagnosis potentially mediate intrinsic resistance to EGFR inhibi-
procedure. Increasingly, mutation-based decision-making procedures are being tors97, highlighting the complexity of possible resistance
integrated in the clinic, and we expect that additional novel technology platforms that mechanisms. It is conceivable that the comprehen-
stratify tumours according to the specific metabolome, epigenome and immune profile sive acquisition of information on different aspects of
of each patient will be applied in the clinic in the near future. The anticipated challenge tumour biology, such as genomic and kinase profiling in
is how best to verify and use the vast amounts of sequencing information for translation patients, will be crucial in the future to determine the best
to the clinic. Ongoing efforts seek to optimize data mining that will link existing course of treatment following any new diagnosis or the
genomic and biological data with clinical databases. In 2013, the Broad Institute, development of acquired resistance.
Cambridge, Massachusetts, USA, launched a global alliance that intends to share
Most patients with advanced stage NSCLC without
genomic and clinical data. A similar effort at Vanderbilt University, Nashville, Tennessee,
USA, which is mediated by a publicly accessible website (My Cancer Genome),
targetable genomic alterations are still treated by conven-
emphasizes the clinical application of cancer research. Worldwide efforts, such as the tional chemotherapies. Activating KRAS mutations were
International Cancer Genome Consortium (ICGC) and the Catalogue of Somatic identified and verified long before the discovery of mutant
Mutations in Cancer (COSMIC) from the Sanger Institute, Hinxton, UK, and joint efforts EGFR. However, treatment choices for patients with
in European countries to establish organoid cultures from primary tumours or biopsies KRAS-mutant lung cancer are still very limited. Current
from patients are also under way. Despite these independent efforts to integrate data efforts to treat this subset of patients have been mostly
sets, a more organized programme is needed on the national and international levels. focused on inhibiting common KRAS downstream sig-
The US National Center for Biotechnology Information recently initiated nalling cascades. The RAF–MEK–ERK pathway, which
whole-genome sequencing to identify rare, druggable oncogenic events in patients is activated directly downstream of KRAS, has proven to
who showed isolated but marked responses to certain drugs; this may represent the
be a valid target in both preclinical models and clinical tri-
first exploratory step towards an integrated programme.
als98–100. However, the clinical benefits of MEK inhibitors,
even in combination with other agents, are still somewhat
Unfortunately, acquired resistance to chronic treat- moderate compared to those of target-specific inhibi-
ment often develops within 9–12 months in most patients tors such as erlotinib for patients with activating EGFR
who are treated with kinase inhibitors84,87,88. Therefore, mutations, and the use of MEK inhibitors is associated
patients who have Stage I–IIIA tumours are still treated with additional complications and enhanced toxicity 100.
by surgical resection as a first-line treatment and receive The available preclinical and clinical results present clear
combination chemotherapy as a standard of care, with challenges to the common belief that therapies target-
the use of targeted agents still considered to be experi- ing one or a few specific alterations should have fewer
mental. For patients with advanced disease who have side effects and lower toxicity compared to standard
progressed on an inhibitor of EGFR or ALK, several chemotherapies. Indeed, this is not entirely a surprise,
recurrent secondary mutations have been identified, such as many of the targeted pathways for lung cancer treat-
as EGFR‑T790M and additional kinase domain mutations ment are also essential for normal tissue functions. The
in ALK87,88. Hence, finding treatments for tumours that simultaneous inhibition of multiple signalling pathways
are resistant to first-generation EGFR or ALK inhibi- can be deleterious to necessary normal cells. One pos-
tors has been a recent focus. Several newly developed sible remedy being explored is to optimize treatment
inhibitors that either have more potency or are ration- schedules and improve targeting efficiencies for single-
ally designed to favourably target the mutated kinases, pathway inhibition by improving inhibitor potency or
such as AZD9291 and CO‑1686 for EGFR and LDK378 linear inhibition of multiple targets within the pathway.
for EML4–ALK, have generated promising initial clini- Nonetheless, alternative treatment approaches with less
cal results89–91. Discovery of the mechanisms that under- toxicity and better responses are of immediate need. A few
lie acquired resistance in patients without additional studies have more recently reported the rational design
mutations in the primary driver gene is also greatly of KRAS inhibitors that target the cysteine residue of the
facilitated by high-throughput analytical approaches. common KRAS mutation G12C in lung cancer 101,102, and
Amplifications of ALK and alternative pro-cancerous these are therefore similar to the second-generation EGFR
pathway activations were identified in ALK fusion- inhibitors (such as WZ4002, AZD9291 and CO‑1686)
positive patients who have become resistant to the first- that target EGFR‑T790M. In vitro studies of these KRAS
generation ALK inhibitor crizotinib87. In patients who inhibitors demonstrate a proof of concept 101,102; however,
are resistant to chronic EGFR inhibitor treatment, a wide the in vivo efficacy of these molecules still requires much
EGFR‑T790M range of resistance mechanisms has been reported. These more investigation.
The most common mutation include increased activities of additional kinases owing
(~50%) in the epidermal to MET, HER2 or ERK amplification, additional muta- Targeting multiple cellular compartments in lung can-
growth factor receptor (EGFR)
gene that confers resistance to
tion of PIK3CA (which encodes the PI3K p110α sub­ cer. Similar to KRAS mutations, many newly identified
EGFR tyrosine kinase inhibitors unit) or overexpression of AXL kinase14,92–95. Enhanced potential pro-cancerous changes, such as overexpression
such as erlotinib and gefitinib. NF‑κB signalling activity was also implied as one possible of the transcription factors SOX2 and MYC103–105, present

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Cytotoxic T lymphocyte clear challenges to our current ideas about treatment enable marked perturbation of gene expression within
protein 4 approaches — in cases in which there is no clear drugga- tumour cells to stop tumour growth. The recently devel-
(CTLA4; also known as ble target, what can be done? Furthermore, the short-lived oped bromodomain protein inhibitors have shown effi-
CD152). A surface receptor in vivo efficacy for most if not all existing small molecule cacy in numerous preclinical studies116, including in lung
that transmits inhibitory
signals to T cells.
inhibitors87,106 also advocates more durable treatment cancer 117, and they are currently under evaluation in the
approaches. On the basis of our current understanding, clinic, including in the ongoing Phase I clinical trials
CD73 the more effective approach probably requires therapies NCT01987362 and NCT01587703. Variations in expres-
A cell surface enzyme that that not only target tumour cells but also target other sion as well as recurrent mutations were also reported
generates extracellular
components of the tumour, such as tumour vasculature, for several histone- and DNA-modifying enzymes,
adenosine, which inhibits
T cell function.
tumour-associated fibroblasts and tumour-specific and/or including enhancer of zeste homologue 2 (EZH2), TET
non-specific immune cells. Besides the more recently methyl­cytosine dioxygenase 2 (TET2) and DNA methyl­
CD47 studied PD1–PDL1 inhibitory pathway, other approaches transferase 3A (DNMT3A) in all subtypes of NSCLC28.
The receptor for that intervene with the immune system, such as antibod- In a similar concept, altered metabolism is one of the key
thrombospondin 1 (TSP1).
CD47 is highly expressed in
ies against cytotoxic T lymphocyte protein 4 (CTLA4; also features of cancer cells. Anti-diabetic drugs, insulin-like
many tumour cells. known as CD152), CD73 or CD47, and more sophisticated growth factor 1 receptor (IGF1R) inhibitors and drugs
cellular immune therapies, such as engineered T cell that target glycolysis or lipid, nucleic acid and amino acid
Chimeric antigen receptors therapy using chimeric antigen receptors (CARs), are also synthesis are currently being explored for anti­tumour
(CARs). Genetically engineered
under extensive scrutiny 107–110. More importantly, ongo- activities in NSCLC118–121. Targeting metabolism is cer-
receptors that result in desired
specificity (to tumour cells) in
ing efforts are seeking to discover the best combination tainly promising for cancer control, particularly when
effector T cells. approach that integrates immune therapy with other combined with other approaches. Recent studies have also
therapies. Angiogenesis has long been seen as a possible highlighted connections between TET and IDH, which
CpG island methylator therapeutic window, with many novel therapeutic agents could have resulted in a CpG island methylator phenotype
phenotype
(CIMP). Reflects the genomic
that have been developed or are being developed to clini- (CIMP) in a subset of lung cancer, and this ‘connects the
status that multiple CpG cally target this process, although the overall efficacy of dots’ between epigenetics and metabolism122–124.
islands are methylated anti-angiogenic agents has been modest in unselected
simultaneously, leading to patient cohorts111. Emerging evidence has suggested that Conclusion
epigenetic inactivation of
the combination of immunotherapy and anti-angiogenic The quickened pace of discovery of mechanisms that
different genes, including
tumour suppressors.
agents has potential synergistic effects112,113, pointing to underlie lung cancer development and possible treatments
a new possible avenue to mutually enhance both treat- in the past decade present the opportunity to integrate
ments. In addition to providing key nutrients and oxy- information from multiple approaches for future lung
genated blood, tumour vasculature might have a role cancer treatment. Large amounts of information about the
in supporting TPCs35,114. Similarly, stromal cells such as identity of individual lung tumours are being collected.
fibroblasts have been shown to provide additional signals New and improved functional studies are needed to meet
that support tumour growth and survival, and they may the pace of data set generation, and all of the aspects of
therefore have major roles in primary and acquired treat- tumour heterogeneity — genetic, cellular and epigenetic
ment resistance35,115. Understanding how best to target — need to be integrated to determine better approaches to
these various aspects of the tumour microenvironment make an impact in this devastating disease. We anticipate
would require a high-throughput comparison of changes the future treatment scheme to be a genotype-depend-
in the tumour microenvironment that occur upon single ent, carefully selected combination that would ensure an
and combination treatments. enhanced tumour immune reaction, inhibition of angio-
Targeted therapies might also be able to indirectly genesis and blockade of interactions between tumour cells
regulate tumour growth. Two prominent examples are and stromal cells. Thus, we advocate ‘integrated therapy’,
drugs that target epigenetic enzymes and metabolic in contrast to the current concept of targeted therapy, as
enzymes. Targeting epigenetic enzymes is expected to the future of effective NSCLC treatment.

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